Sequencing applications process large databases of sequences to identify relationships between sequences. DNA and protein data base sequence alignment are among the most important applications in bioinformatics. Increasing interest in studying the structure and the function of DNA, RNA and proteins, and correlating this information with diseases is driving exponential growth in the bioinformatics market. Such information helps researchers to identify drug leads and other therapeutic modalities. However, as the amount of sequence data being examined increases, the computation time of the sequencing applications grows at a staggering rate.